Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011781.1 Kokia drynarioides strain JFW-HI SEQ_126776, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9082
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Found at i:66 original size:3 final size:3
Alignment explanation
Indices: 60--95 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
50 AATATTTTCT
60 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
96 TGATTAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:101 original size:12 final size:13
Alignment explanation
Indices: 63--105 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
53 ATTTTCTTAA
63 TAATAATAATAA-
1 TAATAATAATAAT
75 TAATAATAATAAT
1 TAATAATAATAAT
*
88 TAATAAT-ATGAT
1 TAATAATAATAAT
100 TAATAA
1 TAATAA
106 AAGAAAAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 22 0.76
13 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:1295 original size:59 final size:60
Alignment explanation
Indices: 1205--1459 Score: 299
Period size: 59 Copynumber: 4.3 Consensus size: 60
1195 AAGCTGTCCA
* * *
1205 AAAATT-CCATTTTTAGCCCCGAACT-TCCAAAAA-TCCCATTTTTTACCCCGAAACTTCCC
1 AAAATTACCATTTTTACCCCCGAA-TGTCCAAAAACT-CCATTTTTGACCCCGAAACTTCCT
* * * *
1264 AAAATT-CCATTTTTAGCCTCGAACT-TCCAAAAAATCCATTTTTGACTCCGAAACTTCCT
1 AAAATTACCATTTTTACCCCCGAA-TGTCCAAAAACTCCATTTTTGACCCCGAAACTTCCT
* * **
1323 AAAATTACCA-TTTTACCCCCGAATGTCCAAAAACTTCATTTTCGACTTCGAAACTTCCT
1 AAAATTACCATTTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCCCGAAACTTCCT
* * * *
1382 AAAATTACCA-TTTTACCCCCGAATGTCTAAAAACTCCATTTTTTACCTCGTAACTTCCT
1 AAAATTACCATTTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCCCGAAACTTCCT
1441 AAAATTACCATTTTTACCC
1 AAAATTACCATTTTTACCC
1460 TCGAGAAGCC
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
58 1 0.01
59 163 0.93
60 12 0.07
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (60 bp):
AAAATTACCATTTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACCCCGAAACTTCCT
Found at i:1456 original size:30 final size:28
Alignment explanation
Indices: 1205--1459 Score: 180
Period size: 30 Copynumber: 8.6 Consensus size: 28
1195 AAGCTGTCCA
*
1205 AAAATTCCATTTTTAGCCCCGAACTTCCA
1 AAAATTCCATTTTTA-CCCCGAACTTCCT
* *
1234 AAAATCCCATTTTTTACCCCGAAACTTCCC
1 AAAATTCCA-TTTTTACCCCG-AACTTCCT
* *
1264 AAAATTCCATTTTTAGCCTCGAACTTCCA
1 AAAATTCCATTTTTA-CCCCGAACTTCCT
* *
1293 AAAAATCCATTTTTGACTCCGAAACTTCCT
1 AAAATTCCATTTTT-ACCCCG-AACTTCCT
*
1323 AAAATTACCA-TTTTACCCCCGAA-TGTCCA
1 AAAATT-CCATTTTTA-CCCCGAACT-TCCT
* **
1352 AAAACTT-CATTTTCGACTTCGAAACTTCCT
1 AAAA-TTCCATTTT-TACCCCG-AACTTCCT
1382 AAAATTACCA-TTTTACCCCCGAA-TGT-CT
1 AAAATT-CCATTTTTA-CCCCGAACT-TCCT
* *
1410 AAAAACTCCATTTTTTACCTCGTAACTTCCT
1 -AAAATTCCA-TTTTTACCCCG-AACTTCCT
1441 AAAATTACCATTTTTACCC
1 AAAATT-CCATTTTTACCC
1460 TCGAGAAGCC
Statistics
Matches: 179, Mismatches: 23, Indels: 47
0.72 0.09 0.19
Matches are distributed among these distances:
28 9 0.05
29 73 0.41
30 85 0.47
31 12 0.07
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGAACTTCCT
Found at i:3970 original size:15 final size:15
Alignment explanation
Indices: 3950--4004 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3940 TTTGCTAGTG
3950 TCAAGACAATACAGA
1 TCAAGACAATACAGA
* * *
3965 TCAAGACAGTTCAAGTG
1 TCAAGACAATAC-AG-A
3982 TCAAGACAATACAGA
1 TCAAGACAATACAGA
*
3997 TTAAGACA
1 TCAAGACA
4005 GTTCATACCC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (15 bp):
TCAAGACAATACAGA
Found at i:3987 original size:32 final size:32
Alignment explanation
Indices: 3946--4009 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3936 CACCTTTGCT
3946 AGTGTCAAGACAATACAGATCAAGACAGTTCA
1 AGTGTCAAGACAATACAGATCAAGACAGTTCA
*
3978 AGTGTCAAGACAATACAGATTAAGACAGTTCA
1 AGTGTCAAGACAATACAGATCAAGACAGTTCA
4010 TACCCGTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (32 bp):
AGTGTCAAGACAATACAGATCAAGACAGTTCA
Done.